I was wondering the same thing and found this:http://wiki.bukkit.org/FAQ#What_is_the_difference_between_Bukkit_and_CraftBukkit.3FFrom my take, Bukkit is just a Programming Library of sorts, while CraftBukkit is functioning server that mods run against. I am sure it is more complex then that, but for our uses it should suffice lol.
Yeah, I've been reading through the source, and in more "programmery" terms, it looks like Bukkit is primarily declarations and CraftBukkit is implementation.